[ase-users] Particle_mutations in GA
Steen Lysgaard
stly at dtu.dk
Thu Mar 2 14:08:15 CET 2017
Hi Alexander,
thanks for reporting this error.
It should be fixed when MR !434 goes through. Specifying the number of
mutations (num_muts) should also work now.
Best regards,
Steen
On 2017-03-02 10:51, Alexander Romanov via ase-users wrote:
> Hi,
> We met a strange problem with RandomMutation operator in Genetic
> Algorithm. Information about unit cell
> is periodically missed. Length of our cell is 36 angstroms but we find
> 1 angstrom per
> dimension in some cases
>
> #-------------------------------------------------------------------------------------------------------
> from ase.ga.data import PrepareDB
> from ase.ga.startgenerator import StartGenerator
> from ase.ga.utilities import closest_distances_generator
> from ase.ga.utilities import get_all_atom_types
> import numpy as np
> from ase import Atoms
> from ase.visualize import view
> from ase.constraints import FixAtoms
>
> for x in range(13, 12, -1):
> for y in range(1, 2, 1):
> db_file = 'Cu%d_gadb_v%d.db' % (x,y,)
>
> L = 36.0
>
> cluster = Atoms('Cu',
> cell=(L, L, L),
> pbc=(0., 0., 0.))
> cluster.center()
> for a in cluster:
> a.x=17.25
> a.y=17.25
> a.z=17.25
> #constraint = FixAtoms(mask=[a.symbol == 'Cu' for a in cluster])
> #cluster.set_constraint(constraint)
>
>
> # define the volume in which cluster is optimized
> # the volume is defined by a corner position (p0)
> # and three spanning vectors (v1, v2, v3)
> pos = (0.0, 0.0, 0.0)
> b = 20.0
> cell = np.array([(b, 0, 0), (0, b, 0), (0, 0, b)])
> p0 = np.array([10., 10., 10.])
> v1 = cell[0, :]
> v2 = cell[1, :]
> v3 = cell[2, :]
>
>
> # Define the composition of the atoms to optimize
> atom_numbers = (x-1)* [29]
>
>
> # define the closest distance two atoms of a given species can
> be to each other
> unique_atom_types = get_all_atom_types(cluster, atom_numbers)
> cd = closest_distances_generator(atom_numbers=unique_atom_types,
> ratio_of_covalent_radii=0.7)
>
> # create the starting population
> sg = StartGenerator(slab=cluster,
> atom_numbers=atom_numbers,
> closest_allowed_distances=cd,
> box_to_place_in=[p0, [v1, v2, v3]])
>
> # generate the starting population
> population_size = 20
> starting_population = [sg.get_new_candidate() for i in
> range(population_size)]
>
> # from ase.visualize import view # uncomment these lines
> # view(starting_population) # to see the starting
> population
>
> # create the database to store information in
> d = PrepareDB(db_file_name=db_file,
> simulation_cell=cluster,
> stoichiometry=atom_numbers)
>
> for a in starting_population:
> d.add_unrelaxed_candidate(a)
>
> #-------------------------------------------------------------------------------------------------------
> from __future__ import print_function
> from random import random
> from ase.io <http://ase.io> import write
> from ase.optimize import BFGS
> from ase.calculators.emt import EMT
> from ase.io <http://ase.io> import read
>
> from ase.ga.data import DataConnection
> from ase.ga.population import Population
> from ase.ga.standard_comparators import InteratomicDistanceComparator
> from ase.ga.cutandsplicepairing import CutAndSplicePairing
> from ase.ga.utilities import closest_distances_generator
> from ase.ga.utilities import get_all_atom_types
> from ase.ga.offspring_creator import OperationSelector
> from ase.ga.standardmutations import MirrorMutation
> from ase.ga.standardmutations import RattleMutation
> from ase.ga.standardmutations import PermutationMutation
> from ase.ga.particle_mutations import RandomMutation
>
> # Change the following three parameters to suit your needs
> population_size = 20
> mutation_probability = 0.3
> n_to_test = 200
>
> for x in range(13, 12, -1):
> for y in range(1, 2, 1):
> # Initialize the different components of the GA
> da = DataConnection('Cu%d_gadb_v%d.db' % (x,y,))
> atom_numbers_to_optimize = da.get_atom_numbers_to_optimize()
> n_to_optimize = len(atom_numbers_to_optimize)
> slab = da.get_slab()
> all_atom_types = get_all_atom_types(slab,
> atom_numbers_to_optimize)
> blmin = closest_distances_generator(all_atom_types,
> ratio_of_covalent_radii=0.7)
>
> comp = InteratomicDistanceComparator(n_top=n_to_optimize,
> pair_cor_cum_diff=0.015,
> pair_cor_max=0.7,
> dE=0.02,
> mic=False)
>
> pairing = CutAndSplicePairing(slab, n_to_optimize, blmin)
> mutations = OperationSelector([1., 1., 1.],
> [MirrorMutation(blmin,
> n_to_optimize),
> RattleMutation(blmin,
> n_to_optimize),
> RandomMutation(length=2.,
> num_muts=4)])
>
> # Relax all unrelaxed structures (e.g. the starting population)
> while da.get_number_of_unrelaxed_candidates() > 0:
> a = da.get_an_unrelaxed_candidate()
> a.set_calculator(EMT())
> print('Relaxing starting candidate {0}'.format(a.info
> <http://a.info>['confid']))
> dyn = BFGS(a, trajectory=None, logfile=None)
> dyn.run(fmax=0.05, steps=100)
> a.info <http://a.info>['key_value_pairs']['raw_score'] =
> -a.get_potential_energy()
> da.add_relaxed_step(a)
>
> # create the population
> population = Population(data_connection=da,
> population_size=population_size,
> comparator=comp)
>
> # test n_to_test new candidates
> for i in range(n_to_test):
> print('Now starting configuration number {0}'.format(i))
> a1, a2 = population.get_two_candidates()
> a3, desc = pairing.get_new_individual([a1, a2])
> if a3 is None:
> continue
> da.add_unrelaxed_candidate(a3, description=desc)
>
> # Check if we want to do a mutation
> if random() < mutation_probability:
> confid = a3.info.get('confid')
> a3_mut, desc = mutations.get_new_individual([a3])
> if a3_mut is not None:
> a3_mut.info <http://a3_mut.info>['confid'] = confid
> da.add_unrelaxed_step(a3_mut, desc)
> a3 = a3_mut
>
> # Relax the new candidate
> a3.set_calculator(EMT())
> dyn = BFGS(a3, trajectory=None, logfile=None)
> dyn.run(fmax=0.05, steps=100)
> a3.info <http://a3.info>['key_value_pairs']['raw_score'] =
> -a3.get_potential_energy()
> da.add_relaxed_step(a3)
> population.update()
>
> write('all_candidates_Cu%d_v%d.traj' % (x,y,),
> da.get_all_relaxed_candidates() )
>
>
> _______________________________________________
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> ase-users at listserv.fysik.dtu.dk
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--
Steen Lysgaard
Post doc
Department of Energy Conversion and Storage
Technical University of Denmark
-------------------------------------------
Frederiksborgvej 399, P.O. Box 49
4000 Roskilde
Mobile +45 5194 4886
stly at dtu.dk
http://www.dtu.dk
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